Molecular modeling and experimental approaches toward designing a minimalist protein having Fc-binding activity of Staphylococcal protein A

New insights into the effect of mutations on affibody-Fc interaction, a molecular dynamics simulation approach

Staphylococcal protein A (SpA) domain B (the basis of affibody) has been widely used in affinity chromatography and found therapeutic applications against inflammatory diseases through targeting the Fc part of immunoglobulin G (IgG). We have performed extensive molecular dynamics simulation of 41 SpA mutants and compared their dynamics and conformations to wild type. The simulations revealed the molecular details of structural and dynamics changes that occurred due to introducing point mutations and helped to explain the SPR results. It was observed in some variants a point mutation caused extensive structural changes far from the mutation site, while an effect of some other mutations was limited to the site of the mutated residue. Also, the pattern of hydrogen bond networks and hydrophobic core arrangements were investigated. We figured out mutations that occurred at positions 128, 136, 150 and 153, affected two hydrophobic cores at the interface as well as mutations introduced at positions 129 and 154 interrupted two hydrogen bond networks of the interface, SPR data showed all of these mutations reduced binding affinity significantly. Overall, by scanning the SpA-Fc interface through the large numbers of introduced mutations, the new insights have been gained which would help to design high- affinity ligands of IgG.

Molecular Modeling of the Interaction of Protein L with Antibodies

Protein L (PpL) is a bacterial protein which is used in the affinity chromatography stage of the production of monoclonal antibodies because of its ability to form high affinity complexes with the light chains of immunoglobulins. In the present work, the binding interfaces between one domain of PpL and antigen-binding fragments (Fab) have been investigated adopting molecular dynamics with the aim of determining the binding contribution of the residues located at the Fab-PpL interface. Because it is known that PpL binds antibodies through two distinct binding sites with different affinities, simulations were performed for both sites to determine interaction free energies to assess the relative binding contribution of the two sites. Mutational studies were then performed only on the dominant binding site. The binding free energy was evaluated with the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and umbrella sampling/weighted histogram analysis methods. Key residues for the formation of the dominant binding site complex were identified by means of alanine scanning performed both for the Fab and PpL domains. Residues of the light chain of the antibody that contribute most to binding were found to be located between SER7 and VAL13. Four residues from PpL are important for the stability of the complex: PHE839, LYS840, GLU849, and TYR853. Three residues of PpL that do not contribute to the interaction were mutated to histidine (HIS), which changes its protonation state as a function of pH, to find whether this could allow us to control the binding interaction energy. This can be useful in the elution stage of the affinity chromatography purification of antibodies if PpL is used as a ligand. These residues are GLN835, THR836, and ALA837. Molecular dynamics simulations with both protonated and unprotonated HIS were performed to mimic how changing pH may reflect on protein-ligand interaction energies. The MMPBSA approach was used to evaluate the variation of the affinity of the mutated systems with reference to the wild type. Our results show that these mutations could help in disrupting the complex under acidic conditions without impairing the affinity of PpL for the light chains at higher pHs.

Evaluation and comparison of alternatives to Protein A chromatography Mimetic and hydrophobic charge induction chromatographic stationary phases

In this paper Protein A mimetic and hydrophobic charge induction chromatographic (HCIC) stationary phases are characterized in terms of their protein adsorption characteristics and their selectivity is compared with Protein A chromatography using a set of Chinese hamster ovary-derived monoclonal antibodies and Fc-fusion proteins. Linear retention experiments were employed to compare the selectivities of these resins for both non-IgG model proteins as well as antibodies and the fusion proteins. While none of the non-IgG model proteins were observed to bind to the Protein A resin, most of them did in fact bind to the alternative resins. In addition, while the elution pH was similar for the model proteins and antibodies on the HCIC resin, the mimetic resins did exhibit higher binding for the antibodies under these linear pH gradient conditions. A mixed mode preparative isotherm model previously developed for HCIC was shown to accurately describe the adsorption behavior of the mimetic materials as well. Host cell protein clearance profiles were also investigated under preparative conditions using complex biological feeds and the results indicated that while some selectivity was observed for both the HCIC and the mimetic materials, the purification factors were in general significantly less than those obtained with Protein A. It is important to note, however, that the selectivity of the mimetic and HCIC materials was also observed to be antibody specific indicating that further optimization may well result in increased selectivities for these materials.

Human transcobalamin II receptor binds to Staphylococcus aureus protein A: implications as to its structure and function

Purified human placental transcobalamin II receptor (TC II-R) dimer of molecular mass 124 kDa bound to Sepharose-linked bacterial immunoglobulin (IgG) binding proteins protein A, protein G, and protein A/G. TC II-R dimer was detected directly, by blotting human placental and rabbit and rat kidney membrane proteins with 125I-protein A, or indirectly, using antiserum to TC II-R or IgG-Fc region and 125I-protein. TC II-R antiserum, but not protein A, protein G, protein A/G, or antiserum to the IgG-Fc region, when added to culture medium of human intestinal epithelial Caco-2 cells or umbilical vein endothelial cells, inhibited ligand binding. However, protein A, protein G, protein A/G, or antiserum to the Fc region inhibited the internalization of the ligand TC II-[57Co]cyanocobalamin. Taken together, these studies strongly suggest TC II-R is an IgG-like molecule that contains an Fc-like region which is important in ligand internalization but not binding.

Control of ceramide-induced apoptosis by IGF-1: involvement of PI-3 kinase, caspase-3 and catalase

Insulin-like growth factor-1 (IGF-1) inhibited N-acetylsphingosine (C2-ceramide)-induced HL-60 cell apoptosis via relieving oxidative damage. This inhibitory action of IGF-1 was blocked by a phosphatidylinositol-3 (PI-3) kinase inhibitor wortmannin and enhanced by overexpression of the p110 catalytic subunit of PI-3 kinase. Either IGF-1 pretreatment or PI-3 kinase overexpression restored ceramide-depleted catalase function, and this restoration was inhibited by wortmannin. A catalase inhibitor 3-amino-1h-1, 2, 4-triazole (ATZ) blocked the inhibitory action of IGF-1 on ceramide-induced apoptosis, whereas exogenous purified catalase enhanced it. Ceramide-activated caspase-3 was inhibited by IGF-1/PI-3 kinase and enhanced by wortmannin, while the addition of a specific caspase-3 inhibitor DMQD-CHO significantly enhanced the restoration by IGF-1 of ceramide-depleted catalase function. Moreover, IGF-1 inhibited C2-ceramide-induced decrease of mitochondrial membrane potential, and increase of cytochrome c release, caspase-3 cleavage and caspase-3 activity as judged by PhiPhiLux cleaving method. In summary, these results suggest that IGF-1/PI-3 kinase inhibited C2-ceramide-induced apoptosis due to relieving oxidative damage, which resulted from the inhibition of catalase by activated caspase-3.

Functional dichotomy of a 20-mer and 16-mer peptide derived from Staphylococcus aureus protein A: importance of amino acid sequence

Protein A (PA) of Staphylococcus aureus possesses a wide variety of biological properties such as antitumor, antitoxic, anticarcinogenic, immunomodulatory, antifungal and antiparasitic. Since PA is a foreign protein, it is quite logical to assume that it may be cleaved into smaller peptide fragments in vivo, which may be responsible for the diverse biological activities of whole PA. We have shown that two proteolytic peptide fragments (20-mer and 16-mer) of PA mimics IgG binding and some of the immunomodulatory properties of PA. In the present study, we investigated upon the functional similarity and dissimilarity in these two peptides. The 16-mer peptide induces the production of IL6, IL10, TNFalpha and IL1alpha but it does not have any effect on secretion of IFNgamma and IL4. Whereas 20-mer peptide induces production of TNFalpha, IL1alpha along with induction of IFNgamma but it downregulates IL4, IL6 and IL10 production. IFNgamma to IL4 ratio clearly indicates that the 20-mer peptide induces Th1 type response, whereas 16-mer peptide induces Th0 type response. The 20-mer peptide retains the antitumor property of the native protein (PA) in Ehrlich ascitis tumor model, whereas 16-mer peptide does retain the same property only in vitro. The 16-mer peptide however can activate macrophages to kill Ehrlich ascitis tumor cells in vitro more efficiently than that of 20-mer peptide. Thus both the peptides although derived from same native protein and has had 13 aminoacid residues in common, appears to evoke different reactivites in the immune system. Thus it appears that the IgG binding ability which is seen with the native protein A molecule and also with both 16-mer and 20-mer peptides do not automatically confer upon them the antitumor property, and cytokine producing activities. Thus it appears that all different properties associated with Protein A may not be necessarily associated with its IgG binding abilities.

Identification of model peptides as affinity ligands for the purification of humanized monoclonal antibodies by means of phage display

A proof-of-principle study was initiated to determine whether phage-display technology could be used to identify peptides as leads in the customization of ligands for affinity chromatography and to identify a peptide or peptidomimetic for use as a Protein A alternative in the affinity purification of monoclonal antibodies. The constant region of humanized anti-Tac (HAT), prepared by pepsin digestion and receptor-affinity chromatography, was used as the target for phage display in this study. As such, 20 phage-derived peptide sequences were identified from four rounds of biopanning with two linear phage-display libraries (7-mer, containing 100 copies of 2 x 10(9) sequences and 12-mer, containing 70 copies of 1.4 x 10(9) sequences). Five peptides were synthesized for use as affinity ligands, based on sequence homology to Protein A, sequence redundancy, and amino acid motifs. The best HAT binding immobilized peptide was EPIHRSTLTALL. The best-fit analysis of this peptide sequence with Protein A yielded an alignment well within the Fc binding domain of Protein A. These results suggest that phage display can serve as a tool in the identification of peptides as model ligands for affinity chromatography.

Solution structure of an immunoactive peptide fragment of Staphylococcal protein-A

Staphylococcal protein-A (SpA) is known to bind the Fc fragment of immunoglobin G in vitro and induce a myriad of immunogenic responses in vivo. The latter is ascribed to be due to the interaction of Fc and SpA. It has also been proposed that in vivo proteolytically cleaved fragments of SpA may be functioning in the same manner. One such fragment (EQQNAFYEILHLPNLNEEQR), fragment 8-27 of the B-domain (SpA-B), was recently shown to exhibit in vivo immunogenic response [Sinha, P., Sengupta, J., and Ray, P. K. (1999) Biochem. Biophys. Res. Commun. 258, 141-147]. As a first step towards understanding the mode of interaction of this peptide with the Fc fragment, we have studied the solution conformation of this isolated peptide by CD and NMR. The peptide, with 7 contact residues in the crystal structure of the SpA-B/Fc complex and comprising of mostly helixI and part of helixII of the 3-helix bundle of SpA-B, was found to be present predominantly in extended structure. However it showed nascent turn/helix like conformations around F14 & Y15. These two residues are known to play a vital role in SpA-B/Fc interaction as deciphered from crystal structure and NMR studies of SpA-B/Fc complex and mutational studies. The implications of our results, especially the nascent conformations found around F14 & Y15, in design of SpA-B mimetic small molecules are discussed.

Identification, quantitation, and characterization of biomolecules by capillary electrophoretic analysis of binding interactions

The high resolving power of capillary electrophoresis combined with the specificity of binding interactions may be used with advantage to characterize the structure-function relationship of biomolecules, to quantitate specific analytes in complex sample matrices, and to determine the purity of pharmaceutical and other molecules. We here review recent and innovative methodologies and applications of high resolution affinity electrophoresis within the fields of binding constant determination, structure-activity studies, quantitative microassays, analysis of drug purity and protein conformation, and immobilized affinity ligands. Despite the virtues of these approaches with respect to applicability, resolving power, speed, and low sample consumption, problems remain with respect to analyte identification and low concentration limits of detection. The ongoing development of new detector technologies for capillary electrophoresis such as mass spectrometry, and possibly nuclear magnetic resonance and other spectroscopic methods, is therefore very promising for the continued increased use of affinity capillary electrophoresis.

Functional mimicry of protein A of Staphylococcus aureus by a proteolytically cleaved fragment

Protein A (PA) of Staphylococcus aureus has an array of biological functions, such as antitumor, antitoxic, anticarcinogenic, immunomodulatory, antifungal, and antiparasitic properties. We have already established that a theoretical trypsin-digested peptide fragment of protein A (20-mer) mimics immunomodulatory and IgG binding property of PA. In the present report we have concentrated on a 16-mer chymotryptic fragment of protein A, which has a sequence of 13 amino acids in common with the previously studied 20-mer peptide. Molecular modeling study qualitatively predicted that both 20-mer and 16-mer peptides retain Fc binding ability from an interaction energy point of view. In the present study our aim was to understand whether this theoretically predicted 16-mer chymotryptic fragment could be formed in a real experiment and also to understand its biological activities. Chymotrypsin cleavage of PA at 37 degrees C for 24 h produced four major fragments on reverse-phase HPLC. The amino acid analyses of each fragment show the absence of cysteine residue from all fragments, which justifies the absence of cysteine in PA. We also observed high content of aspartic acid and glutamic acid residues in all fragments. On gel-filtration chromatography the chymotrypsin cleavage of PA shows five peaks, one of which overlaps with our theoretically selected 16-mer peptide on superimposition. We verified the IgG binding capacity of 16-mer peptide by capillary electrophoresis. The 16-mer peptide also induces the production of TNFalpha and IL-1alpha in serum of mice. The above observations suggest that the 16-mer peptide may be produced by chymotrypsin cleavage and also that this peptide possesses some of the major biological properties of PA, such as IgG binding, TNFalpha and IL-1alpha elicitation, etc.